**1. Introduction**

The protozoan *T. cruzi* is the causative agent of Chagas disease and affects approximately 7 million people, mostly in Central and South America, where another 18 million people live at risk of infection [1]. This parasite exhibits a complex life cycle varying between the nonreplicative/infective form, known as the trypomastigote (bloodstream in mammalian host and metacyclic inside the vector), and the replicative forms, known as the amastigote (in the mammalian host) and

epimastigote (in the invertebrate vector). Morphological and metabolic changes are observed among these life forms with the presence of distinct proteomic [2,3] and transcriptomic [4] profiles. However, the control of gene expression in *T. cruzi* relies largely on posttranscriptional and translation levels since transcription does not occur from a specific RNA pol II promoter for each gene but, rather, nonrelated genes are transcribed as a unique polycistron and then trans-spliced into individual mature mRNA molecules [5]. Therefore, other levels of gene expression regulation stand out, such as mRNA processing [6], translational repression [7–9], polysome recruitment [10], and codon adaptation [11,12]. In this scenario, noncoding DNA may also be involved as a regulatory element in mRNA expression [10–13].

Among coding and noncoding DNA, the *T. cruzi* genome presents at least 50% repetitive sequences, which include multigenic families, retrotransposons and subtelomeric repeats [14–16]. Of the repetitive DNA elements found within intergenic regions, most have no identified function to date. For example, satellite DNA is a 195 bp repetitive element that can be used as a *T. cruzi* infection marker in molecular diagnostics [17]; however, no function has been attributed to this sequence. Conversely, multigenic families mostly encode surface proteins involved in cell invasion as well as immune system evasion by *T. cruzi* [18]. The expression levels of these genes vary along the *T. cruzi* life cycle according to their function, but little is known about how they are regulated.

The 3′UTR (untranslated region) from mRNA and RNA binding proteins (RNA-BP) has emerged as a key factor in mRNA stability and protein expression level regulation in *T. cruzi*, including some proteins from multigenic families [19–21]. In this study, we developed a new strategy to identify new repetitive elements in the *T. cruzi* genome and found an intergenic repetitive sequence located downstream of many genes of multigenic families, such as mucin-associated proteins (MASPs) and trans-sialidases. Using RNAseq analysis, we confirmed that this sequence is present on the 3′UTRs of these mRNAs and is correlated with gene expression regulation, indicating that this repetitive sequence may have a cis-regulatory function on the expression of multigenic family mRNAs.
